(...After some time working on another project). Thank you for your replies. I did look at the "Timer Synchronization", but unfortunately, this talks about using one timer to trigger another, something that I could see how to do it.... here we want one channel to trigger another from the same timer. My feeling is that this cannot be done. I just need to convince my hardware engineer who designed it that way ;-)

it is not possible to start second pulse "exactly" when the first pulse ends but the SHIFT can be minimized with some custom code. have a look at RM0008 reference manual > Timer Synchronization (article 13.3.15 - page 296)